This work proposes a method for numerically investigating the fracture mechanism of cement paste at the microscale based on X-ray computed tomography and nanoindentation. For this purpose, greyscale level based digital microstructure was generated by X-ray microcomputed tomography with a resolution of 2 μm/voxel length. In addition, statistics based micromechanical properties (i.e. Young's modulus and hardness) were derived from the grid nanoindentation test which was set to have an interaction volume the same as the resolution of the digital microstructure. A linear relationship between the two probability density functions of greyscale level and local Young's modulus was assumed and verified by the two-sample Kolmogorov-Smirnov (K–S) statistic. Based on this assumption, the fracture and deformation of a digital cubic volume with a dimension of 100 μm under uniaxial tension was simulated using a lattice fracture model. In addition, the influence of heterogeneity on fracture response was studied. Furthermore, the proposed method was compared with the results obtained from a traditional approach used previously by the authors in which discrete phases (capillary pore, anhydrous cement clinker, outer and inner hydration products) were considered. The two methods show similar crack patterns and stress-strain responses. The proposed method is regarded more promising as it captures also the gradient of material properties (within the discrete phases) in the cement paste.